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    Characterising CG5846 (Peep) in Drosophila melanogaster neural function : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2024) Wilson, Sarah Jean
    Histone deacetylase 4 (HDAC4) is a transcriptional regulator that has been implicated in a number of neurodevelopmental and neurodegenerative diseases that are associated with intellectual disability, cognitive defects, and/or memory loss. Both the accumulation of nuclear HDAC4 and its loss-of-function have been linked to these conditions, therefore exploring HDAC4’s role in neuronal function is essential to understand the molecular mechanisms underlying these diseases. In Drosophila, overexpression of HDAC4 results in defects in morphogenesis of axons in the mushroom body, a structure essential for memory formation, as well as long-term memory defects and disruption to the development of the compound eye. The molecular mechanisms underlying these HDAC4-induced phenotypes are currently unknown. RNA-sequencing on fly heads in which HDAC4 was overexpressed has previously been performed and showed few genes were transcriptionally regulated by HDAC4. In addition, an enhancer/suppressor rough eye phenotype screen has also been performed which identified a number of genes that interact genetically in the same molecular pathway as HDAC4. To further investigate the molecular mechanisms underlying HDAC4 dysfunction, an RNA interference (RNAi) based candidate screen for potential HDAC4-interactors was performed, which involved quantification of developmental defects in the mushroom body and eye following RNAi knockdown of each candidate. It was hypothesised that if a phenotype resulting from RNAi knockdown was similar to that induced by HDAC4 overexpression, that candidate may function in similar molecular pathways. A single candidate-interactor was selected (CG5846, named Peep) for further investigation. On overexpression, Peep and HDAC4 co- distribute in nuclei of mushroom body neurons, however no physical interaction was detected. Furthermore, overexpression of Peep did not rescue the HDAC4-induced mushroom body or eye defects. Due to the uncharacterised nature of Peep, a thorough investigation was performed to assess the importance of Peep in survival, longevity, motor function, brain development, courtship learning and memory, and wing development. Peep was observed to be essential for survival of glial cells and for normal mushroom body development, which warrants further investigation. Reduced expression of Peep also resulted in a unique severe necrotic eye phenotype, and through this, Peep was shown to play a potential role in processes involved in regulating mitochondrial and proteasomal function, apoptosis and oxidative stress. These data provide the first documented characterisation of the functional role of Peep in Drosophila development and provide the basis for further investigation into the underlying molecular mechanisms involved in mushroom body and eye development.
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    Investigating HDAC4 aggregation in a Drosophila model of neuronal development : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2024-06-21) Hawley, Hannah Rose
    Histone deacetylase four (HDAC4) is essential in neuronal development and function, and dysregulation of HDAC4 has been observed in a number of neurodevelopmental and neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. In particular, its aberrant nuclear accumulation is a common feature among these diseases, and it has been observed that upon upregulation or accumulation in the nucleus, HDAC4 forms punctate foci in neuronal nuclei. Previous research in a Drosophila model determined that overexpression of HDAC4 disrupted both neuronal development and long-term memory, and this was largely mediated by the nuclear pool of HDAC4. Based on these data, it was hypothesised that aggregates of HDAC4 are responsible for the neurotoxicity that leads to disrupted neurodevelopment and memory. Therefore, this study aimed to determine whether the presence of HDAC4 nuclear aggregates correlated with neurodevelopmental deficits in a Drosophila model of neurodevelopment, and if so, how they mediate their toxic effects. The N-terminus of HDAC4 forms homo-oligomers in solution, and it was hypothesised that full-length HDAC4 similarly oligomerises, and that this is required for its aggregation in neuronal nuclei. Mutations predicted to prevent oligomerisation were introduced into the N- terminus of HDAC4 and were shown to significantly reduce aggregation of HDAC4 in Drosophila neurons. Furthermore, their presence also reduced the severity of HDAC4 overexpression-induced impairments in neurodevelopment. Conversely, stabilisation of oligomerisation increased aggregation and the severity of neurodevelopmental phenotypes, together indicating that aggregation positively correlates with the severity of neurodevelopmental deficits. HDAC4 aggregates have been previously shown to sequester the transcription factor MEF2, and further investigation revealed that the presence of MEF2 stabilised aggregation and increased the severity of defects in neuronal development. Importantly, targeting the interaction between HDAC4 and MEF2 reduced the severity of these defects. Other than MEF2, the composition of HDAC4 aggregates is unknown, and therefore immunoprecipitation-coupled mass spectrometry was performed on nuclear HDAC4 to identify candidate interactors of aggregates. This revealed a number of proteins with roles in neuronal development and function, as well as those involved in splicing and protein homeostasis, suggesting that aggregates may be impairing these processes to mediate toxicity. Together these data indicate that nuclear aggregation of HDAC4 impairs neurodevelopment, and may constitute a novel biomarker of disease or therapeutic target. Given the overlap in aetiology between neurodevelopmental and neurodegenerative diseases, further investigation of whether HDAC4 aggregation contributes to the severity and/or progression of neurodegenerative disorders is warranted.
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    Teasing apart the interaction between HDAC4 and Ankyrin2 in Drosophila neuronal function : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry, School of Fundamental Sciences, Massey University, Manawatu, New Zealand
    (Massey University, 2021) Wilson, Sarah Jean
    Histone deacetylase 4 (HDAC4) is a class IIa histone deacetylase that has previously been implicated in a range of neurodevelopmental and neurodegenerative diseases which involve deficits in memory and cognition. Overexpression of HDAC4 in the Drosophila brain impairs memory, therefore making Drosophila an ideal genetic model system to further investigate the molecular pathways through which HDAC4 acts. A recent genetic screen in Drosophila for genes that interact in the same molecular pathway as HDAC4 identified the cytoskeletal regulator Ankyrin2 (Ank2). The Ank2 protein plays a pivotal role in maintaining the stability and plasticity of the spectrin-actin cytoskeleton by organising the distribution of ion channels and cell adhesion molecules, which is essential to normal learning and memory formation. Both overexpression of HDAC4 and knockdown of Ank2 result in similar deficits in Drosophila brain development and long-term memory formation, suggesting that these two proteins may interact together in such processes. HDAC4 contains an N-terminal ankyrin repeat binding motif and it was hypothesised that HDAC4 interacts physically with the ankyrin repeat region at the N-terminus of Ank2, however, no physical interaction was detected via co-immunoprecipitation. Further investigation was then carried out to elucidate the nature of the genetic interaction proposed between HDAC4 and Ank2. In doing so, it was observed that nuclear accumulation of HDAC4 is required for this interaction, however, the presence of the HDAC4 ankyrin repeat binding motif is not required. This is consistent with the finding that HDAC4 does not bind Ank2 and indicates that the interaction between HDAC4 and Ank2 is indirect. It was also identified that Ank2 and HDAC4 are both required for Drosophila eye development as knockdown of Ank2 paired with overexpression of HDAC4 resulted in a severe novel "blueberry" phenotype that has not yet been characterised for these genes. Furthermore, it was observed that Ank2 was required for normal growth and morphogenesis of dendrites in the visual system, whereby both knockdown of Ank2 and overexpression of HDAC4 disrupt dendrite morphogenesis. These data provide further understanding of the roles of HDAC4 and Ank2 in Drosophila neuronal function, and the establishment of the molecular pathway in which HDAC4 and Ank2 act will be essential in unravelling additional mechanisms involved in the processes of learning and memory.
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    Investigating the role of HDAC4 subcellular distribution in Drosophila development and memory : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Biochemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2019) Main, Patrick James
    The class IIa histone deacetylase HDAC4 has been previously demonstrated to play an essential role in brain development, learning and memory. However, the molecular pathways through which it acts are unknown. HDAC4 undergoes activity-dependent nucleocytoplasmic shuttling, disruption of the balance of nuclear and cytoplasmic HDAC4 has been identified as a factor in developmental and neurodegenerative disorders. This project used Drosophila melanogaster as a model to investigate the effects of altered subcellular distribution of HDAC4 on neural development and memory formation through the overexpression of Drosophila HDAC4 and wild-type human HDAC4 (hHDAC4), as well as nuclear- and cytoplasm-localising mutants of hHDAC4 named 3SA and L175A, respectively. The nuclear or cytoplasmic abundance of HDAC4 was adjusted by expressing the mutants during development or in adult flies. It was established that increased nuclear abundance of hHDAC4 in the brain impaired long-term memory and development, whereas increasing the cytoplasmic abundance did not. Further investigation showed that, contrary to vertebrate models, HDAC4 does not appear to repress memory in Drosophila through inactivation of MEF2 or CREB. Investigation of the transcriptomic changes induced by nuclear and cytoplasmic HDAC4 via RNASeq on RNA isolated from fly heads showed that L175A unexpectedly up-regulates the expression of genes in transcription and DNA synthesis. The relatively low number of transcriptional changes induced by 3SA suggested that it may be acting through largely transcriptionally independent means to impair memory and development in Drosophila. The localisation of HDAC4 to punctate foci in nuclei, potentially forming protein aggregates similar to Marinesco bodies seen in Parkinson’s Disease warrants further investigation. This project has shown that nuclear but not cytoplasmic HDAC4 impairs development and memory in Drosophila. Furthermore, cytoplasmic HDAC4 may play a role in transcriptional regulation of neurons, possibly regulation metabolic activity, suggesting that the activity-dependent nucleocytoplasmic shuttling of HDAC4 may not be primarily to remove HDAC4 from the nucleus and but instead to return HDAC4 to the cytoplasm.
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    Evolution of the spherical cell shape in bacteria : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University, Albany, New Zealand
    (Massey University, 2019) Yulo, Paul Richard Jesena
    Cell shape is an important feature of bacterial cells. It is involved in critical aspects of bacterial cell biology such as motility, growth, and the evasion of predators. Despite this, how cell shape has evolved in bacteria is unclear. For most rod-shaped bacteria, the maintenance of cell shape depends primarily on the bacterial actin-like protein, MreB. In this study, we show that the deletion of MreB from the rod-shaped model organism Pseudomonas fluorescens SBW25 results in the formation of aberrant spherical cells that have increased size and reduced fitness. This new MreB-null strain (ΔmreB) is susceptible to mechanical damage and grows poorly due to cell division defects. Furthermore, synthesized peptidoglycan (PG) chains were shorter and cell wall assembly was disorganised in this strain. A 1,000-generation evolution experiment comprised of multiple independent lineages produced spherical cells that have a reduced cell size and improved fitness. Mutations in the PG synthesis protein PBP1a were found across multiple lineages. Genetic reconstructions demonstrated that these mutations have a loss-of-function effect that reduced PG cross-linking and restored the ordered assembly of the cell wall, thereby reducing cell size and improving fitness in MreB-null cells. In one lineage, a five-gene deletion that included the gene coding for the outer membrane channel OprD was found to be beneficial. This deletion reduced cell size, improved fitness, and restored orderly cell wall construction. The mechanism responsible for this is unknown, but it may be related to modifications in septum localisation via the Min system. Finally, we show using phylogenetic analysis that PBP loss is a general trend in bacteria that evolved to become spherical, hinting at a plausible strategy for the evolution of the spherical cell shape from rod-shaped progenitors.